Merge branch 'dev-define-engines-abc' into dev-convert-modelabc-to-torch-nn-model

Author: shaneahmed

.github/workflows/mypy-type-check.yml

@@ -40,7 +40,7 @@ jobs:
         mypy --install-types --non-interactive --follow-imports=skip \
           tiatoolbox/__init__.py \
           tiatoolbox/__main__.py \
-          tiatoolbox/typing.py \
+          tiatoolbox/type_hints.py \
           tiatoolbox/tiatoolbox.py \
           tiatoolbox/utils \
           tiatoolbox/tools \

.github/workflows/python-package.yml

@@ -30,7 +30,7 @@ jobs:
         sudo apt update
         sudo apt-get install -y libopenslide-dev openslide-tools libopenjp2-7 libopenjp2-tools
         python -m pip install --upgrade pip
-        python -m pip install ruff==0.8.2 pytest pytest-cov pytest-runner
+        python -m pip install ruff==0.9.4 pytest pytest-cov pytest-runner
         pip install -r requirements/requirements.txt
     - name: Cache tiatoolbox static assets
       uses: actions/cache@v3

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
         - mdformat-black
         - mdformat-myst
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.21
+    rev: 0.7.22
     hooks:
     - id: mdformat
       # Optionally add plugins
@@ -60,7 +60,7 @@ repos:
       - id: rst-inline-touching-normal # Detect mistake of inline code touching normal text in rst.
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.8.6
+    rev: v0.9.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

pre-commit/notebook_urls.py

@@ -197,7 +197,9 @@ def check_notebook(
         for line_num, line in enumerate(cell["source"]):
             new_line = replace_line(line, to_ref, replacements)
             if new_line != line:
-                print(f"{path.name}: Changed (cell {cell_num+1}, line {line_num+1})")
+                print(
+                    f"{path.name}: Changed (cell {cell_num + 1}, line {line_num + 1})"
+                )
                 changed = True
                 cell["source"][line_num] = new_line
     return changed, notebook

requirements/requirements_dev.txt

@@ -10,7 +10,7 @@ pytest>=7.2.0
 pytest-cov>=4.0.0
 pytest-runner>=6.0
 pytest-xdist[psutil]
-ruff==0.8.2  # This will be updated by pre-commit bot to latest version
+ruff==0.9.4  # This will be updated by pre-commit bot to latest version
 toml>=0.10.2
 twine>=4.0.1
 wheel>=0.37.1

tests/engines/test_engine_abc.py

@@ -355,7 +355,7 @@ def test_engine_run() -> NoReturn:
 
 def test_engine_run_with_verbose() -> NoReturn:
     """Test engine run with verbose."""
-    """Run pytest with `-rP` option to view progress bar on the captured stderr call"""
+    # Run pytest with `-rP` option to view progress bar on the captured stderr call.
 
     eng = TestEngineABC(model="alexnet-kather100k", verbose=True)
     out = eng.run(
@@ -401,7 +401,7 @@ def test_patch_pred_zarr_store(tmp_path: pytest.TempPathFactory) -> NoReturn:
     )
     assert Path.exists(out), "Zarr output file does not exist"
 
-    """ test custom zarr output file name"""
+    # Test custom zarr output file name
     eng = TestEngineABC(model="alexnet-kather100k")
     out = eng.run(
         images=np.zeros((10, 224, 224, 3), dtype=np.uint8),

tests/models/test_models_abc.py

@@ -70,7 +70,6 @@ def forward(self: Proto) -> None:
     # skipcq
     def infer_batch() -> None:
         """Define infer batch."""
-        pass  # base class definition pass  # noqa: PIE790
 
 
 @pytest.mark.skipif(

tests/test_annotation_stores.py

@@ -40,7 +40,7 @@
 if TYPE_CHECKING:  # pragma: no cover
     from numbers import Number
 
-    from tiatoolbox.typing import Geometry
+    from tiatoolbox.type_hints import Geometry
 
 
 sqlite3.enable_callback_tracebacks(True)  # noqa: FBT003

tests/test_docs.py

@@ -141,7 +141,7 @@ def raise_source_exception(
         for n, line in enumerate(source.splitlines())
     ]
     if source_offset:
-        source_lines.insert(source_lineno, f"{' '*(source_offset+3)}^ {message}")
+        source_lines.insert(source_lineno, f"{' ' * (source_offset + 3)}^ {message}")
     annotated_source = "\n".join(source_lines)
     exception = type(exception) if exception else SyntaxError
     msg = f"{rel_path}:{file_lineno}: {message}\n{annotated_source}"

tests/test_patch_extraction.py

@@ -21,7 +21,7 @@
 )
 
 if TYPE_CHECKING:
-    from tiatoolbox.typing import IntPair, Resolution, Units
+    from tiatoolbox.type_hints import IntPair, Resolution, Units
 
 
 def read_points_patches(